10-100372754-C-T

Variant names:

• chr10-100372754-C-T
• rs569184
• ENST00000693438.2:n.640G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693438.2(ENSG00000289301):​n.640G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,016 control chromosomes in the GnomAD database, including 4,153 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (4153 hom., cov: 32)
• Consequence: ENSG00000289301 ENST00000693438.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

ENSG00000289301 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289301	ENST00000693438.2	n.640G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29275 AN: 151898 Hom.: 4140 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.193 AC: 29320 AN: 152016 Hom.: 4153 Cov.: 32 AF XY: 0.192 AC XY: 14266 AN XY: 74302

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0994

Gnomad4 OTH AF: 0.157

Alfa AF: 0.129 Hom.: 437

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.74
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs569184; hg19: chr10-102132511;